Perturbing the energy landscape for improved packing during computational protein design

A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures

(2020) Jianfu Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

Comparison of Rosetta flexible‐backbone computational protein design methods on binding interactions

(2019) Amanda L. Loshbaugh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency

(2017) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Algorithms for protein design

(2016) Pablo Gainza et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Computational design of self-assembling cyclic protein homo-oligomers

(2016) Jorge A. Fallas et al.   Nature Chemistry

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

(2015) Noah Ollikainen et al.   PLoS Computational Biology

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Automated selection of stabilizing mutations in designed and natural proteins

(2012) B. Borgo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

(2012) Grant S. Murphy et al.   STRUCTURE

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY